findExcl: Find branches that are non-overlapping with specified...

In fionarhuang/treeclimbR: An algorithm to find optimal signal levels in a tree

Find branches that are non-overlapping with specified branches in a tree

Description

Find all branches whose leaves do not overlap with those of the specified branches.

Usage

findExcl(tree, node, use.alias = FALSE)

Arguments

tree	A phylo object.
node	A numeric or character vector specifying the nodes.
use.alias	A logical scalar. If TRUE, the alias name is used to name the output vector.

Value

A vector of node numbers

Author(s)

Ruizhu Huang

Examples

suppressPackageStartupMessages({
    library(ggtree)
    library(TreeSummarizedExperiment)
})

data(tinyTree)
ggtree(tinyTree, branch.length = "none") +
    geom_text2(aes(label = node)) +
    geom_hilight(node = 17, fill = "blue", alpha = 0.3) +
    geom_hilight(node = 13, fill = "orange", alpha = 0.3)

## Find branches whose leaves do not overlap with the two colored branches.
## The returned branches are represented at the highest tree level
## possible without including any of the forbidden branches.
findExcl(tree = tinyTree, node = c(17, 13))

fionarhuang/treeclimbR documentation built on May 19, 2024, 1:18 p.m.